Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Many-particle charged-particle plasma simulations using spatial meshes for the electromagnetic field solutions, particle-in-cell (PIC) merged with Monte Carlo collision (MCC) calculations, are coming into wide use for application to partially ionized gases. The author emphasizes the development of PIC computer experiments since the 1950s starting with one-dimensional (1-D) charged-sheet models, the addition of the mesh, and fast direct Poisson equation solvers for 2-D and 3-D. Details are provided for adding the collisions between the charged particles and neutral atoms. The result is many-particle simulations with many of the features met in low-temperature collision plasmas; for example, with applications to plasma-assisted materials processing, but also related to warmer plasmas at the edges of magnetized fusion plasmas. >

Particle-in-Cell Charged Particle Simulations, plus Monte Carlo Collisions with Neutral Atoms, PIC-MCC

A simple electrical model for biological cells predicts an increasing probability for electric field interactions with cell substructures of prokaryotic and eukaryotic cells when the electric pulse duration is reduced into the sub-microsecond range. The validity of this hypothesis was verified experimentally by applying electrical pulses with electric field intensities of up to 5.3 MV/m to human eosinophils in vitro. When 3-5 pulses of 60 ns duration were applied to human eosinophils, intracellular granules were modified without permanent disruption of the plasma membrane. In spite of the extreme electrical power levels applied to the cells thermal effects could be neglected because of the ultrashort pulse duration. The intracellular effect extends conventional electroporation to cellular substructures and opens the potential for new applications in apoptosis induction, gene delivery to the nucleus, or altered cell functions, depending on the electrical pulse conditions.

Intracellular effect of ultrashort electrical pulses.

Electric phenomena play an important role in biophysics. Bioelectric processes control the ion transport processes across membranes, and are the basis for information transfer along neurons. These electrical effects are generally triggered by chemical processes. However, it is also possible to control such cell functions and transport processes by applying pulsed electric fields. This area of bioengineering, bioelectrics, offers new applications for pulsed power technology. One such application is prevention of biofouling, an effect that is based on reversible electroporation of cell membranes. Pulsed electric fields of several kV/cm amplitude and submicrosecond duration have been found effective in preventing the growth of aquatic nuisance species on surfaces. Reversible electroporation is also used for medical applications, e.g. for delivery of chemotherapeutic drugs into tumor cells, for gene therapy, and for transdermal drug delivery. Higher electric fields cause irreversible membrane damage. Pulses in the microsecond range with electric field intensities in the tens of kV/cm are being used for bacterial decontamination of water and liquid food. A new type of field-cell interaction, "Intracellular Electromanipulation", by means of nanosecond pulses at electric fields exceeding 50 kV/cm has been recently added to known bioelectric effects. It is based on capacitive coupling to cell substructures, has therefore the potential to affect transport processes across subcellular membranes, and may be used for gene transfer into cell nuclei. There are also indications that it triggers intracellular processes, such as programmed cell death, an effect, which can be used for cancer treatment. In order to generate the required electric fields for these processes, high voltage, high current sources are required. The pulse duration needs to be short to prevent thermal effects. Pulse power technology is the enabling technology for bioelectrics. The field of bioelectrics, therefore opens up a new research area for pulse power engineers, with fascinating applications in biology and medicine.

Bioelectrics-new applications for pulsed power technology

A review of mainly the past two years is undertaken of the industrial applications of pulsed power. Repetitively operated pulsed power generators with a moderate peak power have been developed for industrial applications. These generators are reliable and have low maintenance. Development of the pulsed power generators helps promote industrial applications of pulsed power for such things as food processing, medical treatment, water treatment, exhaust gas treatment, ozone generation, engine ignition, ion implantation and others. Here, industrial applications of pulsed power are classified by application for biological effects, for pulsed streamer discharges in gases, for pulsed discharges in liquid or liquid- mixture, and for material processing.

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Industrial Applications of Pulsed Power Technology

Today's ultrafast, pulse generators are capable of producing high-voltage pulses, (>1 kV), with fast, leading-edge rise times, (<1 ns). A review of generator implementation methods is presented that includes a detailed discussion of the various circuit designs and a list of commercially available high-voltage pulse generators. All of these generators are capable of rise times less than a few ns and voltages greater than several hundred volts. Finally, a brief description of the three primary switch types, reed, spark gap, and solid state is presented.

A review of short pulse generator technology

The electrical characteristics and design features of a low inductance, compact, 500 kV, 500 J, 10 Hz repetition rate Marx generator for driving an high-power microwave (HPM) source are discussed. Benefiting from the large energy density of mica capacitors, four mica capacitors were utilized in parallel per stage, keeping the parasitic inductance per stage low. Including the spark-gap switches, a stage inductance of 55 nH was measured, which translates with 100 nF capacitance per stage to ∼18.5Ω characteristic Marx impedance. Using solely inductors, ∼1mH each, as charging elements instead of resistors enabled charging the Marx within less than 100 ms with little charging losses. The pulse width of the Marx into a matched resistive load is about 200 ns with 50 ns rise time. Repetitive HPM generation with the Marx directly driving a small virtual cathode oscilator (Vircator) has been verified. The Marx is fitted into a tube with 30 cm diameter and a total length of 0.7 m. We discuss the Marx operation at up...

Design and optimization of a compact, repetitive, high-power microwave system

Present-day ultra-wideband radiation sources produce Megavolt pulses at hundreds of picosecond (ps) risetimes. Empirical data on the breakdown characteristics for dielectric media at these short time lengths and high voltages are either extremely limited or nonexistent. In support of the design of these ultra-wideband sources, we are investigating the breakdown characteristics, at these voltages and time lengths, of several liquids and high-pressure gases. These include air, N/sub 2/, H/sub 2/, SF/sub 6/, and transformer oil. Gap voltages attained were over 700 kV and gas pressures were over 150 atm (15 MPa). Breakdown times achieved were on the order of 600 ps. Electric field strengths observed for given breakdown times were higher than predicted by other investigators. An empirical fit is presented for the data obtained.

High voltage subnanosecond breakdown

We are fabricating and testing several different types of cathodes for the same vircator driven by a single shot Marx generator and pulse forming line (300 kV, 60 ns, 30 Omega). The cathodes types, each with an emitting area of ~32 cm2, include the original velvet with a new geometry, carbon fiber, pin-array, and an array of all metal cathodes. The metal cathodes are made from aluminum and oxygen free copper fashioned to similar geometries with either a chemical etch or a CNC machining process. The vircator is tested with all of these cathodes using both polarity configurations and evaluated for beam voltage, current density, microwave output, and single shot lifetime. In addition to the cathode testing, several stainless steel and tungsten anode meshes with varying transparencies (50% - 80%) are evaluated. The construction and testing of an anode fashioned from Tantalum (70% transparency) is also discussed. Electron beam uniformity of the metal cathodes is investigated with the emitted electron beam current-density distribution evaluated in both time and space. Optimization of output power using resonant effects is also examined.

Cathode and Anode Optimization in a Virtual Cathode Oscillator

Gyromagnetic Nonlinear Transmission Lines (NLTLs) generate microwaves through the damped gyromagnetic precession of the magnetic moments in ferrimagnetic material, and are thus utilized as compact, solid-state, frequency agile, high power microwave (HPM) sources. The output frequency of a NLTL can be adjusted by control of the externally applied bias field and incident voltage pulse without physical alteration to the structure of the device. This property provides a frequency tuning capability not seen in many conventional e-beam based HPM sources. The NLTLs developed and tested are mesoband sources capable of generating MW power levels in the L, S, and C bands of the microwave spectrum. For an individual NLTL the output power at a given frequency is determined by several factors including the intrinsic properties of the ferrimagnetic material and the transmission line structure. Hence, if higher power levels are to be achieved, it is necessary to combine the outputs of multiple NLTLs. This can be accomplished in free space using antennas or in a transmission line via a power combiner. Using a bias-field controlled delay, a transient, high voltage, coaxial, three port, power combiner was designed and tested. Experimental results are compared with the results of a transient COMSOL simulation to evaluate combiner performance.

John J. Mankowski

Papers

A review of short pulse generator technology

Design and optimization of a compact, repetitive, high-power microwave system

High voltage subnanosecond breakdown

Cathode and Anode Optimization in a Virtual Cathode Oscillator

Bias-field controlled phasing and power combination of gyromagnetic nonlinear transmission lines.